All ABS systems I'm aware of, auto & bike, require special procedures to bleed the ABS pump (that doohickey under the right side cover). The procedure involves using the new Digital Technician II to operate the pump and valves while bleeding the system.
I spent a lot of years in auto assembly plants, and for many of those years drove a different vehicle home every night for quality evaluation. When ABS became standard, I noticed a difference in brake pedal feel, a slightly softer feel with slightly more travel. However, I also noted quite a bit of variation from one vehicle to another. It appeared that even with the evacuate and fill system we used (automated equipment pulls a vacuum on the system and then pumps fluid into it under pressure), air was being trapped in the ABS pump on some units. When those units were bled properly in the repair bay, pedal feel was improved to the point of being very close to that of a non-ABS unit. The point of all this rambling is that I would recommend anyone who has the new ABS and excessive travel or softness at the lever have the dealer perform the ABS specific bleeding procedure outlined in the manual. Make sure you watch the process, and if they don't hook up the Digital Tech computer, they aren't doing it correctly and it won't help the issue.
What you are feeling may or may not be normal for an ABS equipped model, and unless you are such an optimist that you really believe H-D would never ship a bike out the door with a problem, having the brake system properly bled would be a quick and painless process that any halfway decent dealership should be happy to perform if for no other reason than to give you peace of mind.
Jerry